- Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Volume covered by a group of atoms
by Thomas Goddard 13 May '10

13 May '10

Hi Miguel, For creating the volume occupancy map the molmap command creates a volume by placing a Gaussian centered at each atom. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html The Gaussian width is set by the molmap resolution parameter and is the same for all atoms. It does not use vdw radii. If you want to use vdw radii and if you want to sum over many torsion angles you might use a modified version of the molmap Python code. See the molecule_grid_data() routine in file chimera/share/MoleculeMap/molmap.py in your Chimera distribution. Tom > Hi Eric and Tom, > > Thank you! Yes, I would like to improve the script so, it would be great > if you can give me pointers about clashes and filling the VDW space! > > Also, just a question: is there a way to access bonds as part of a tree? > I would like to select the atoms implicitly from the list of bonds to be > rotated. > > Best regards, > > > Miguel > > Le 13 mai 2010 à 02:15, Eric Pettersen a écrit : > >> Hi Miguel, >> The script still is pretty useful! I've added it to the "Python >> Scripts" page on our wiki (Scripts – Chimera >> <http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts>). You are >> right that improvements could be made, but it's a nice starting point. >> If you ever decide to refine the script, I could probably provide >> pointers on finding clashes, whereas Tom Goddard (whom I've cc'ed) >> would probably have to be the one to assist in filling a grid based on >> the atom's VDW radius (presumably scaling a three-dimensional gaussian >> or some such). >> >> --Eric >> >> On May 12, 2010, at 1:46 PM, Miguel Ortiz Lombardia wrote: >> >>> Le 12 mai 2010 à 19:00, Eric Pettersen a écrit : >>> >>>> Hi Miguel, >>>> I'm glad you got everything sorted out. Good luck. Feel free to >>>> shoot me any further questions you might have. >>>> >>>> --Eric >>>> >>> >>> Hi Eric, >>> >>> Thanks! I managed to make it work. I'm attaching the script in case >>> you or someone may find it useful. There is only a point I haven't >>> managed to solve: as it is, the script creates a grid point at the >>> atom center positions, while I would be more interested in the van >>> der Waals volume. Nevertheless, since this is a very naive approach >>> (it would be more interesting, for example, to avoid any clashes) I'm >>> using an external set of programs (mapman and mama from the "Uppsala >>> Software Factory") to extend this volume by a couple of grid points. >>> >>> I'm attaching as well a figure so you see how it looks like (after >>> expansion with mapman/mama). >>> >>> Thanks for your advice, I have learnt a lot from this exercise. >>> >>> Best regards, >>> >>> >>> -- Miguel >>> >>> Architecture et Fonction des Macromolécules Biologiques (UMR6098) >>> CNRS, Universités d'Aix-Marseille I & II >>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France >>> Web: http://www.pangea.org/mol/spip.php?rubrique2 >>> >>> >>> <C3vol.png><torspace.py> >>> >>> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is >> believed to be clean. > > -- Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Web: http://www.pangea.org/mol/spip.php?rubrique2 > > > > >

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Re: [chimera-dev] [Chimera-users] Volume covered by a group of atoms
by Eric Pettersen 11 May '10

11 May '10

On May 9, 2010, at 10:14 PM, Miguel Ortiz Lombardia wrote: > Dear all, > > I would like to represent as a volume the space that would be > covered by a set of atoms that are bound by "torsionable" bonds when > one systematically modifies those torsion angles. An example would > be the side-chain of an amino acid; imagine I would like to have a > glimpse of what part of the space could be occupied by that side- > chain. As a first approximation I wouldn't care about clashes. > > I would appreciate if someone can point me to an existing way of > obtaining such representation or to an algorithm that could be > implemented within chimera (which I would be happy to share with > other interested people; if I manage to code it, that's it!) Hi Miguel, This problem has two parts: adjusting the torsions and visualizing the result. Adjusting the Torsions If you're adjusting the chi angles of an amino acid, then this is easy in Chimera. Each such residue has chi1/chi2/chi3 attributes that you can set, e.g.: for chi1 in range(0, 360, 10): r.chi1 = chi1 for chi2 in range(0, 360, 10): r.chi2 = chi2 for chi3 in range(0, 360, 10): r.chi3 = chi3 do something You'd probably actually want to write the code as a recursive routine, since otherwise it is awkward to handle the fact that some residues have different numbers of chi angles than others. You might also want to change your angle increment based on the recursion depth. If you're changing torsions that aren't the well-known amino acid chi angles, then you'll have to resort to Chimera's more generic torsion- adjustment facilities, the core of which are in the BondRotMgr module. Specifically, if 'b' is the bond you want to adjust, then: from BondRotMgr import bondRotMgr torsion = bondRotMgr.rotationForBond(b) and then torsion.increment(amount) will increment the torsion angle by 'amount' degrees (from its current position). If you want to set the dihedral to a certain value (rather than just increment from the current position) then you will have to measure the dihedral you care about with: chimera.dihedral(a1.xformCoord(), a2.xformCoord(), a3.xformCoord(), a4.xformCoord()) and then use the appropriate increment value, or use chimera.phipsi._setAngle(bond, newAngle, curAngle) [in the latter case you don't have to call rotationForBond yourself]. Visualizing the Result There are a bunch of possibilities of course. I'll touch on two: a bunch of spheres, and an actual volume. 1) As you change the torsion, you can use each atom's .coord() method to get Point instances which can be used to place helium atoms at those positions with BuildStructure.placeHelium(). You could put the heliums in the same model or in a new model (by providing a model name to your first call of placeHelium()). 2) Computing a volume is not too hard conceptually. Basically you decide on a grid spacing and then make a dictionary that maps xyz grid addresses to occupancy counts (omitting counts of zero). Then you find the lower and upper bounds for each axis, create a 3D array with corresponding dimensions, and populate that array with your counts. Then you can open that in Volume Viewer and use all the Volume Viewer facilities to look at the occupancy. There is code that does just this in Movie.gui, it's MovieDialog's computeVolume method. The line: gridData = {} initializes the occupancy-count dictionary and the loop that immediately follows that populates the dictionary. Most of the loop isn't relevant for you (getting the right coordinate set and adjusting for "hold selection steady") but the very end of the loop is, the part that maps coordinates into xyz grid addresses and adjusts the corresponding count. Then after that the loop the "generate volume" and "show volume" sections are largely relevant. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Tiled Wall Display Extension
by christopher lau 05 May '10

05 May '10

Hi, I have developed a Tiled Wall Display Extension for ViewDock in Chimera. I was in contact with Greg and Tom during the summer regarding development of the extension. According to the Chimera license agreement it states that we need to contact the developers directly and seek permission to distribute files that modify the original Chimera source code. Can we receive permission to allow our code to be publicly available via our website? P.S. I did not release the URL of our website on this list-serv because we haven't received official approval from Chimera. Best Regards, Christopher Lau UCSD, Department of Bioengineering

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Re: [chimera-dev] [Chimera-users] place fragment (again)
by Eric Pettersen 04 May '10

04 May '10

On May 4, 2010, at 7:44 AM, Elisabeth Ortega wrote: > Dear all, > > We are trying to place a fragment in an exact position. We created a > fragment with tetrahedral symmetry and we are trying to link an atom > of > other molecule at 2.00 A of the central atom of the new fragment and > making a certain angle (120 degrees for example) with one of the > substituents to get the correct orientation of the new fragment. > > Has anybody an idea that how can we do that? Hi Elisabeth, I think you'll find that you've under-defined the positioning -- I think you'll need another angle and a dihedral at least to uniquely position the fragment, but nonetheless I can provide some code to get you pointed in the right direction. First, of course, you would use placeFragment() to get your fragment to some (arbitrary) initial position. The function will return a Residue that contains your fragment's atoms. From this you can find the central atom, etc. So let's say you've found the relevant atoms for positioning and you have these variables: fca = central fragment atom fsa = fragment substituent atom (for angle positioning) oa = atom from other atom (for distance) r = fragment residue --- start code --- # make fca-oa distance 2.0 [assumes fragment in same model as other molecule] dv = fca.coord() - oa.coord() dv.length = 2.0 - dv.length for a in r.atoms: a.setCoord(a.coord() + dv) # make fsa-fca-oa angle 120 from chimera import cross, angle, Point, Xform fscrd, fccrd, ocrd = [a.coord() for a in (fsa, fca, oa)] axis = cross(fscrd-fccrd, fccrd-ocrd) # axis the rotation will be around delta = 120.0 - angle(fscrd, fccrd, ocrd) v = fccrd - Point(0.0, 0.0, 0.0) # rotation is about origin, so move center atom there trans1 = Xform.translation(v) # translation to origin v.negate() trans2 = Xform.translation(v) # translation back from origin trans1.multiply(Xform.rotation(axis, delta)) trans1.multiply(trans2) for a in r.atoms: a.setCoord(trans1.apply(a.coord())) --- end code --- If your initial positioning of the fragment places the center atom in the proper direction from the other molecule atom you may be able to get away with only one angle (may still need a dihedral though). I am working on a function for bonding molecules together that would have been helpful here but it isn't done yet (the partially-completed function is bind() which you can look at in BuildStructure/ __init__.py). Also, I cc'ed chimera-dev on this and redirected replies there since this is pretty programming intensive. Good luck and don't hesitate to ask more questions. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] ChemGroups
by Eric Pettersen 27 Apr '10

27 Apr '10

On Apr 27, 2010, at 7:05 AM, Mauro Truglio wrote: > Hi, > I got to understand the syntax to edit and even create "new" > chemical groups for chimera to select (I successfully edited the > file __init__.py in ChemGroups). Now I'm facing this problem with > aromatic amines: when selecting, for example, primary aromatic > amine, I'd like to include also che C atom in the selection - not > only N,H,H. > With other chemical groups this was easy, thanks to the [1,1,1,0,1]- > like notation. But these aromatic amines are described in a > different way, through the function findAroAmines in miscFind.py, > and I'm finding it difficult to edit it. > Can you help me? Hi Mauro, Yes, it wasn't easy (or maybe even possible) to describe aromatic amines (and a few other groups) using the notation used for most groups -- they required a custom function. Nonetheless the change you desire is pretty simple. In the part of the code that finds the aromatic carbon attached to the nitrogen, also add the carbon to the list of atoms included in the amine. So this code: if bonded.element.number == ChemGroup.C: boundCarbons = boundCarbons + 1 if bonded.idatmType == 'Car': boundAro = True continue if bonded.idatmType == 'C3': continue becomes: if bonded.element.number == ChemGroup.C: boundCarbons = boundCarbons + 1 if bonded.idatmType == 'Car': boundAro = True amine.append(bonded) continue if bonded.idatmType == 'C3': continue If you want all the bonded carbons, not just the aromatic one, put a similar line in the "if bonded.idatmType == 'C3':" conditional. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. Directed followups to chimera-dev, since this discussion is pretty "programmery"

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Re: [chimera-dev] [Chimera-users] placeFragment
by Eric Pettersen 26 Apr '10

26 Apr '10

On Apr 26, 2010, at 3:36 AM, Elisabeth Ortega wrote: > Dear all, > > I'm trying to place a fragment in certain position. I did this (on > Python IDLE): > > from BuildStructure import placeFragment > > placeFragment( fragment, resName, model = 'scratch', position=None) > > > Where fragment = benzene and resName = RING6 but I am not sure about > that . > Could you give me an example of placeFragment code? Hi Elisabeth, This will place a benzene ring at the center of the view in a new residue named "BZN" in a new model named "scatch": from BuildStructure import placeFragment from BuildStructure.Fragment import RING6, fragDict placeFragment(fragDict[RING6]["benzene"], "BZN") Let me know if you have more questions. Though the placeFragment function does have some documentation, the Fragment.py file doesn't. Sorry about that. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. I cc'ed the chimera-dev mailing list on this since that list deals more with programming questions.

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run chimera's IDLE in terminal on mac os x
by ylei＠ecs.umass.edu 24 Feb '10

24 Feb '10

Dear all How to run Chimera's IDLE(i.e. python shell) in terminal on the system of mac? Thanks. Yang

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run chimera in terminal on mac os x
by ylei＠ecs.umass.edu 24 Feb '10

24 Feb '10

Dear all Could somebody tell me how to run Chimera in terminal on the system of mac? Thanks. Yang

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No glue!
by Jean Didier Pie Marechal 17 Feb '10

17 Feb '10

Dear all, I'd like to add an atom at the mass center of each aromatic fragment of my ligand (I always want to add an atom don't I?). I know how to calculate cm, put an atom or point, select aromatic ring BUT I am banging my head against the wall to define one entity of each ring separately. Would it be a lot more complicate to do so for any cyclic moeity. Thanks for any help! best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Gener 28, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 9 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. ribbon for circular molecule (Volodymyr Babin) > 2. Re: ribbon for circular molecule (Thomas Goddard) > 3. Re: ribbon for circular molecule (Thomas Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 27 Jan 2010 23:48:46 -0500 (EST) > From: "Volodymyr Babin" <vbabin(a)ncsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] ribbon for circular molecule > Message-ID: <53249.152.1.53.169.1264654126.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Sirs, > > I am writing to ask for the chimera sources -- I would like to > visualize a circular molecule using ribbons. As far as I can tell, > with the current code ribbons always have ends (cannot be closed) > because of the following snipped from > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > 696 Molecule::updateRibbonData() > 697 { > 698 clearRibbonData(); > 699 > 700 // > 701 // For each residue, find the residues before > and after. 702 > // Note that only residues with valid guide and plane atoms > 703 > // may be used as the prev/next residue in a ribbon. > 704 // > 705 std::map<Residue *, RibbonResidue> rrMap; > 706 Residue *prev = NULL; > ^^^^^^^^^^^^^^^^^^^^^ > > Could you please allow me to check out the svn version of the > chimera or get (easily compilable) sources of a recent release. > > Thank you, > > Volodymyr > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 28 Jan 2010 10:58:34 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61DE5A.6050907(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Volodymyr, > > Chimera is not easy to compile because it requires about 40 > third-party libraries as described on the Chimera source code page > (link > is on the Chimera download page). > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > Also there is a bit of third-party surface calculation code which > we are > not allowed to distribute. All the source code is viewable with > the web > interface to the SVN repository. We also have a ticket active for > allowing public access to check-out the entire Chimera SVN tree > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > but that has not been done yet. > > If your purpose is to make a figure that doesn't have a gap in > the > circular molecule then the following trick might achieve that. You > could make a new molecule that is not closed and has the two > starting > residues duplicated at the end (with increasing residue numbers). > Then > when you show the ribbon there will be an overlapping stretch. > Because > the overlap will not be perfect you can hide the ribbon for one of > each > duplicated residue. If you add a couple duplicate residues the > ribbon > should come into exact alignment with itself. > > I've added your request for circular ribbons to our feature > request list. > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > If you can live with circular cross-section tube a command like > > shape tube :1-125.A@CA:1.A@CA radius 1 > > could do it but it does not close nicely -- different tangent > vector and > coloring and selection is not as flexible -- the tube is just a > surface > model. > > Tom > > > > Dear Sirs, > > > > I am writing to ask for the chimera sources -- I would like to > > visualize a circular molecule using ribbons. As far as I can tell, > > with the current code ribbons always have ends (cannot be closed) > > because of the following snipped from > > > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > > > 696 Molecule::updateRibbonData() > > 697 { > > 698 clearRibbonData(); > > 699 > > 700 // > > 701 // For each residue, find the residues before > and after. 702 > > // Note that only residues with valid guide and plane atoms > 703 > > // may be used as the prev/next residue in a ribbon. > > 704 // > > 705 std::map<Residue *, RibbonResidue> rrMap; > > 706 Residue *prev = NULL; > > ^^^^^^^^^^^^^^^^^^^^^ > > > > Could you please allow me to check out the svn version of the > > chimera or get (easily compilable) sources of a recent release. > > > > Thank you, > > > > Volodymyr > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > ------------------------------ > > Message: 3 > Date: Thu, 28 Jan 2010 11:38:01 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61E799.3070708(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Volodymyr, > > I will try to get public SVN download of Chimera source working. > It > would be great if you learned about programming Chimera. This > particular part of the code is especially difficult though because > the > ribbon class is produced by an antiquated in-house C++ code > generation > tool called OTF (Object Technology Framework). I'll add you to the > notification list for the SVN access ticket. > > Tom > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Volodymyr Babin > To: Thomas Goddard > Date: 1/28/10 11:16 AM > > > Hi Thomas, > > > > thank you for a very detailed reply. > > > >> Also there is a bit of third-party surface calculation code > which we are > >> not allowed to distribute. > > > > I understand that. I probably was imprecise: it would be nice to be > > able to compute everything but the non-distributable code. > > > >> If your purpose is to make a figure that doesn't have a gap > in the > >> circular molecule then the following trick might achieve that. You > >> could make a new molecule that is not closed and has the two > starting>> residues duplicated at the end (with increasing residue > numbers). Then > >> when you show the ribbon there will be an overlapping stretch. > Because>> the overlap will not be perfect you can hide the ribbon > for one of each > >> duplicated residue. If you add a couple duplicate residues the > ribbon>> should come into exact alignment with itself. > > > > Thank you. I tried this before looking at the sources. I have not > tried> it with the circular cross-section tube though ... thanks. > > > >> I've added your request for circular ribbons to our feature request > >> list. > > > > Thank you. I am not sure this is something of general interest and > > therefore ruled out this option (feature request) deciding to play > > with it myself. I am new to chimera and must admit that its > visualization> capabilities are absolutely outstanding ... which is > another reason > > I would prefer to learn it through. > > > > Thank you & best regards, > > > > Volodymyr > > > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Thomas Goddard > To: Volodymyr Babin > Date: 1/28/10 10:58 AM > > > Hi Volodymyr, > > > > Chimera is not easy to compile because it requires about 40 > > third-party libraries as described on the Chimera source code > page (link > > is on the Chimera download page). > > > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > > > Also there is a bit of third-party surface calculation code which > we are > > not allowed to distribute. All the source code is viewable with > the web > > interface to the SVN repository. We also have a ticket active > for > > allowing public access to check-out the entire Chimera SVN tree > > > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > > > but that has not been done yet. > > > > If your purpose is to make a figure that doesn't have a gap in > the > > circular molecule then the following trick might achieve that. > You > > could make a new molecule that is not closed and has the two > starting > > residues duplicated at the end (with increasing residue numbers). > Then > > when you show the ribbon there will be an overlapping stretch. > Because > > the overlap will not be perfect you can hide the ribbon for one > of each > > duplicated residue. If you add a couple duplicate residues the > ribbon > > should come into exact alignment with itself. > > > > I've added your request for circular ribbons to our feature > request list. > > > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > > > If you can live with circular cross-section tube a command like > > > > shape tube :1-125.A@CA:1.A@CA radius 1 > > > > could do it but it does not close nicely -- different tangent > vector and > > coloring and selection is not as flexible -- the tube is just a > surface > > model. > > > > Tom > > > > > >> Dear Sirs, > >> > >> I am writing to ask for the chimera sources -- I would like to > >> visualize a circular molecule using ribbons. As far as I can tell, > >> with the current code ribbons always have ends (cannot be closed) > >> because of the following snipped from > >> > >> libs/_chimera/Chimera.toolkit/Ribbon.implementation > >> > >> 696 Molecule::updateRibbonData() > >> 697 { > >> 698 clearRibbonData(); > >> 699 > >> 700 // > >> 701 // For each residue, find the residues before and > >> after. 702 // Note that only residues with valid guide > and > >> plane atoms 703 // may be used as the prev/next > residue in a > >> ribbon. > >> 704 // > >> 705 std::map<Residue *, RibbonResidue> rrMap; > >> 706 Residue *prev = NULL; > >> ^^^^^^^^^^^^^^^^^^^^^ > >> > >> Could you please allow me to check out the svn version of the > >> chimera or get (easily compilable) sources of a recent release. > >> > >> Thank you, > >> > >> Volodymyr > >> > >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > End of Chimera-dev Digest, Vol 72, Issue 9 > ****************************************** >

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Re: [chimera-dev] No glue!
by Jean Didier Pie Marechal 15 Feb '10

15 Feb '10

Hi Elaine, yes the centroid option is what I would like to do for each aromatic ring. The thing is that I have a small database to screen regarding relative position of this centroids. My main problem is how could I generate automatically a unique group of atoms for each ring and then calculate the centroid afterwards. I have no idea. Thanks for the help, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dissabte, Febrer 13, 2010 8:31 pm Assumpte: Re: [chimera-dev] No glue! > Hi JD, > I can't answer in terms of programming, but thought I would mention > > that in recent daily builds (version 1.5), "Axes/Planes" (under > Tools... Structure Analysis) has been extended to "Axes/Planes/ > Centroids." With this tool, or with the command "define," you can > create a sphere at the optionally mass-weighted centroid of any set > of > atoms. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> > > These centroid objects, although not atoms, can be used in distance > > measurements via the "Axes/Planes/Centroids" GUI or with the > command > "distance." > > Perhaps these centroid objects will meet your needs, so you don't > need > to write this code to create atoms. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Feb 13, 2010, at 6:25 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > I'd like to add an atom at the mass center of each aromatic > fragment > > of my ligand (I always want to add an atom don't I?). > > > > I know how to calculate cm, put an atom or point, select aromatic > > > ring BUT I am banging my head against the wall to define one > entity > > of each ring separately. > > > > Would it be a lot more complicate to do so for any cyclic moeity. > > Thanks for any help! > > best, > > JD >

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getting nuts with aromatic
by Jean Didier Pie Marechal 13 Feb '10

13 Feb '10

Dear all, I'd like to add an atom at the mass center of each aromatic ring of my ligand (I always want to add an atom, don't I?). I know how to calculate cm, put an atom or point, select aromatic ring BUT I am banging my head against the wall to define one entity of each ring separately. I played a while with bonds properties but I can't see the light (Caroline...). If there is a way to do so for aromatic rings, how complicated would it be to do the same for any kind of cyclic moeity. Thanks for any help! best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Gener 28, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 9 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. ribbon for circular molecule (Volodymyr Babin) > 2. Re: ribbon for circular molecule (Thomas Goddard) > 3. Re: ribbon for circular molecule (Thomas Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 27 Jan 2010 23:48:46 -0500 (EST) > From: "Volodymyr Babin" <vbabin(a)ncsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] ribbon for circular molecule > Message-ID: <53249.152.1.53.169.1264654126.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Sirs, > > I am writing to ask for the chimera sources -- I would like to > visualize a circular molecule using ribbons. As far as I can tell, > with the current code ribbons always have ends (cannot be closed) > because of the following snipped from > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > 696 Molecule::updateRibbonData() > 697 { > 698 clearRibbonData(); > 699 > 700 // > 701 // For each residue, find the residues before > and after. 702 > // Note that only residues with valid guide and plane atoms > 703 > // may be used as the prev/next residue in a ribbon. > 704 // > 705 std::map<Residue *, RibbonResidue> rrMap; > 706 Residue *prev = NULL; > ^^^^^^^^^^^^^^^^^^^^^ > > Could you please allow me to check out the svn version of the > chimera or get (easily compilable) sources of a recent release. > > Thank you, > > Volodymyr > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 28 Jan 2010 10:58:34 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61DE5A.6050907(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Volodymyr, > > Chimera is not easy to compile because it requires about 40 > third-party libraries as described on the Chimera source code page > (link > is on the Chimera download page). > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > Also there is a bit of third-party surface calculation code which > we are > not allowed to distribute. All the source code is viewable with > the web > interface to the SVN repository. We also have a ticket active for > allowing public access to check-out the entire Chimera SVN tree > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > but that has not been done yet. > > If your purpose is to make a figure that doesn't have a gap in > the > circular molecule then the following trick might achieve that. You > could make a new molecule that is not closed and has the two > starting > residues duplicated at the end (with increasing residue numbers). > Then > when you show the ribbon there will be an overlapping stretch. > Because > the overlap will not be perfect you can hide the ribbon for one of > each > duplicated residue. If you add a couple duplicate residues the > ribbon > should come into exact alignment with itself. > > I've added your request for circular ribbons to our feature > request list. > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > If you can live with circular cross-section tube a command like > > shape tube :1-125.A@CA:1.A@CA radius 1 > > could do it but it does not close nicely -- different tangent > vector and > coloring and selection is not as flexible -- the tube is just a > surface > model. > > Tom > > > > Dear Sirs, > > > > I am writing to ask for the chimera sources -- I would like to > > visualize a circular molecule using ribbons. As far as I can tell, > > with the current code ribbons always have ends (cannot be closed) > > because of the following snipped from > > > > libs/_chimera/Chimera.toolkit/Ribbon.implementation > > > > 696 Molecule::updateRibbonData() > > 697 { > > 698 clearRibbonData(); > > 699 > > 700 // > > 701 // For each residue, find the residues before > and after. 702 > > // Note that only residues with valid guide and plane atoms > 703 > > // may be used as the prev/next residue in a ribbon. > > 704 // > > 705 std::map<Residue *, RibbonResidue> rrMap; > > 706 Residue *prev = NULL; > > ^^^^^^^^^^^^^^^^^^^^^ > > > > Could you please allow me to check out the svn version of the > > chimera or get (easily compilable) sources of a recent release. > > > > Thank you, > > > > Volodymyr > > > > > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > ------------------------------ > > Message: 3 > Date: Thu, 28 Jan 2010 11:38:01 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > To: Volodymyr Babin <vbabin(a)ncsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] ribbon for circular molecule > Message-ID: <4B61E799.3070708(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Volodymyr, > > I will try to get public SVN download of Chimera source working. > It > would be great if you learned about programming Chimera. This > particular part of the code is especially difficult though because > the > ribbon class is produced by an antiquated in-house C++ code > generation > tool called OTF (Object Technology Framework). I'll add you to the > notification list for the SVN access ticket. > > Tom > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Volodymyr Babin > To: Thomas Goddard > Date: 1/28/10 11:16 AM > > > Hi Thomas, > > > > thank you for a very detailed reply. > > > >> Also there is a bit of third-party surface calculation code > which we are > >> not allowed to distribute. > > > > I understand that. I probably was imprecise: it would be nice to be > > able to compute everything but the non-distributable code. > > > >> If your purpose is to make a figure that doesn't have a gap > in the > >> circular molecule then the following trick might achieve that. You > >> could make a new molecule that is not closed and has the two > starting>> residues duplicated at the end (with increasing residue > numbers). Then > >> when you show the ribbon there will be an overlapping stretch. > Because>> the overlap will not be perfect you can hide the ribbon > for one of each > >> duplicated residue. If you add a couple duplicate residues the > ribbon>> should come into exact alignment with itself. > > > > Thank you. I tried this before looking at the sources. I have not > tried> it with the circular cross-section tube though ... thanks. > > > >> I've added your request for circular ribbons to our feature request > >> list. > > > > Thank you. I am not sure this is something of general interest and > > therefore ruled out this option (feature request) deciding to play > > with it myself. I am new to chimera and must admit that its > visualization> capabilities are absolutely outstanding ... which is > another reason > > I would prefer to learn it through. > > > > Thank you & best regards, > > > > Volodymyr > > > > > -------- Original Message -------- > Subject: Re: [chimera-dev] ribbon for circular molecule > From: Thomas Goddard > To: Volodymyr Babin > Date: 1/28/10 10:58 AM > > > Hi Volodymyr, > > > > Chimera is not easy to compile because it requires about 40 > > third-party libraries as described on the Chimera source code > page (link > > is on the Chimera download page). > > > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > > > Also there is a bit of third-party surface calculation code which > we are > > not allowed to distribute. All the source code is viewable with > the web > > interface to the SVN repository. We also have a ticket active > for > > allowing public access to check-out the entire Chimera SVN tree > > > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641 > > > > but that has not been done yet. > > > > If your purpose is to make a figure that doesn't have a gap in > the > > circular molecule then the following trick might achieve that. > You > > could make a new molecule that is not closed and has the two > starting > > residues duplicated at the end (with increasing residue numbers). > Then > > when you show the ribbon there will be an overlapping stretch. > Because > > the overlap will not be perfect you can hide the ribbon for one > of each > > duplicated residue. If you add a couple duplicate residues the > ribbon > > should come into exact alignment with itself. > > > > I've added your request for circular ribbons to our feature > request list. > > > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > > > > If you can live with circular cross-section tube a command like > > > > shape tube :1-125.A@CA:1.A@CA radius 1 > > > > could do it but it does not close nicely -- different tangent > vector and > > coloring and selection is not as flexible -- the tube is just a > surface > > model. > > > > Tom > > > > > >> Dear Sirs, > >> > >> I am writing to ask for the chimera sources -- I would like to > >> visualize a circular molecule using ribbons. As far as I can tell, > >> with the current code ribbons always have ends (cannot be closed) > >> because of the following snipped from > >> > >> libs/_chimera/Chimera.toolkit/Ribbon.implementation > >> > >> 696 Molecule::updateRibbonData() > >> 697 { > >> 698 clearRibbonData(); > >> 699 > >> 700 // > >> 701 // For each residue, find the residues before and > >> after. 702 // Note that only residues with valid guide > and > >> plane atoms 703 // may be used as the prev/next > residue in a > >> ribbon. > >> 704 // > >> 705 std::map<Residue *, RibbonResidue> rrMap; > >> 706 Residue *prev = NULL; > >> ^^^^^^^^^^^^^^^^^^^^^ > >> > >> Could you please allow me to check out the svn version of the > >> chimera or get (easily compilable) sources of a recent release. > >> > >> Thank you, > >> > >> Volodymyr > >> > >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > End of Chimera-dev Digest, Vol 72, Issue 9 > ****************************************** >

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ribbon for circular molecule
by Volodymyr Babin 28 Jan '10

28 Jan '10

Dear Sirs, I am writing to ask for the chimera sources -- I would like to visualize a circular molecule using ribbons. As far as I can tell, with the current code ribbons always have ends (cannot be closed) because of the following snipped from libs/_chimera/Chimera.toolkit/Ribbon.implementation 696 Molecule::updateRibbonData() 697 { 698 clearRibbonData(); 699 700 // 701 // For each residue, find the residues before and after. 702 // Note that only residues with valid guide and plane atoms 703 // may be used as the prev/next residue in a ribbon. 704 // 705 std::map<Residue *, RibbonResidue> rrMap; 706 Residue *prev = NULL; ^^^^^^^^^^^^^^^^^^^^^ Could you please allow me to check out the svn version of the chimera or get (easily compilable) sources of a recent release. Thank you, Volodymyr

2 2

calculate volume major blob
by Jean Didier Pie Marechal 24 Jan '10

24 Jan '10

Dear all, I need to do the work for thousands of structures, so Iam interesting in a scripting solution here. After a surfnet calculation on a given atom selection, my script select the whole surface model and calculates the volume of the all bunch. However, I'd like to have the volume of the major blob only. On the other hand, for a given number of structures, I would like to remove all minor blobs blobs so that only the major one remains on the screen. How could I do this second step? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

2 1

extensions outside the chimera directory
by Jean Didier Pie Marechal 22 Jan '10

22 Jan '10

Dear All, I am preparing a series of practical for a MSc and I'd like a series of extensions I have to be accessible for students. Unfortunately, I do not have write access to the /usr/local/chimera directory of the pcs of the classrom and the OS images the machines boot on are not upgradable easily. Could I locate extensions in a user directory? Sorry for my ignorance.... Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Gener 20, 2010 9:00 pm Assumpte: Chimera-dev Digest, Vol 72, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. StructureSequence.residues change (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 19 Jan 2010 13:22:31 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] StructureSequence.residues change > Message-ID: <BE4EE11C-A560-4D1D-A08B-5ED3AA052CF5(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > I've made a change in the 1.5 build that could affect > script/extension > writers that use the StructureSequence.residues list. That list > can > now contain None values. This is because now the sequence is the > full > sequence if available in SEQRES records even if some of the > corresponding structure is missing. Such missing structure has > None > for the Residue value. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu >

2 1

StructureSequence.residues change
by Eric Pettersen 19 Jan '10

19 Jan '10

I've made a change in the 1.5 build that could affect script/extension writers that use the StructureSequence.residues list. That list can now contain None values. This is because now the sequence is the full sequence if available in SEQRES records even if some of the corresponding structure is missing. Such missing structure has None for the Residue value. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

(no subject)
by Mojie Duan 19 Jan '10

19 Jan '10

Dear Chimera Developers, I needs to calculate the inter-helical angle for thousands of conformations. We know Chimera can calculate the inter-helical angle for one conformation. We are wondering if Chimera can calculate the inter-helical angle for all these conformations at one time? or would you please point out how to write a script to do this? Thanks. Mojie

2 1

Calculating RMSD
by Victor Muñoz 15 Jan '10

15 Jan '10

Hi, I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong? Thanks for your help.

2 1

adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Hi everyone, I have obtained cavities for a given atom selection using surfnet and I want to put an atom at the centroid of the main blob. I know how to do this for a selected set of atom but I am struggling with the surfaces. At this point, I splitted it (accelator Sc) and then I can select the blob I am interested in. But how could I create a particular object for this blob? From there, how could I add an atom (i.e. helium) and the centroid of the blob? Thanks for any help, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimarts, Desembre 15, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 71, Issue 4 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > 2. Re: [Chimera-users] Programmer's Guide feedback.... (Tom > Goddard) 3. Re: [Chimera-users] Programmer's Guide feedback.... > (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 15 Dec 2009 10:55:42 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide > feedback.... > Message-ID: <61EC3E93-8EE5-48E0-AB71-4705D5162EE4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote: > > > 4. The ToolbarButton.py doesn't work unless the "import re" and > > > "import chimera" are in the function body. This is because > Chimera > > deletes all globals after loading a file. This has often been a > > headache for me and Chimera should not delete globals. > > This is a behavior of Python. We load scripts into their own > temporary module to avoid pollution of the Chimera main namespace > (e.g. if the script defined globals named "id" or "sum" or "type" > they > would override built-in functions of the same name for all future > script executions!). When Chimera unloads the temporary module, > Python nulls out it's global namespace (to give garbage collection > a > shot at working). > > Now perhaps Chimera shouldn't unload the module. I think this > would > be a reasonable change. Perhaps it could be discussed at our next > internal Chimera developers' meeting to ensure that I'm not > forgetting > any other ramifications that the change might have. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

3 2

Re: [chimera-dev] [Chimera-users] Programmer's Guide feedback....
by Eric Pettersen 15 Dec '09

15 Dec '09

On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote: > 4. The ToolbarButton.py doesn't work unless the "import re" and > "import chimera" are in the function body. This is because Chimera > deletes all globals after loading a file. This has often been a > headache for me and Chimera should not delete globals. This is a behavior of Python. We load scripts into their own temporary module to avoid pollution of the Chimera main namespace (e.g. if the script defined globals named "id" or "sum" or "type" they would override built-in functions of the same name for all future script executions!). When Chimera unloads the temporary module, Python nulls out it's global namespace (to give garbage collection a shot at working). Now perhaps Chimera shouldn't unload the module. I think this would be a reasonable change. Perhaps it could be discussed at our next internal Chimera developers' meeting to ensure that I'm not forgetting any other ramifications that the change might have. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 2

odd plugin crash
by Mark Moll 09 Dec '09

09 Dec '09

I have a plugin for Chimera that uses its own binary python module. The module is statically linked against the system python2.5 library on Snow Leopard. When I select my plugin, Chimera crashes. Attached is the crash report with Chimera 1.4 (it happens with build 28940 and probably other versions as well). However, if I open Chimera from the command line like so: open /Users/mmoll/Downloads/Chimera.app then there is no crash. The module is linked against the following libraries: otool -L ~/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so /Users/mmoll/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so: /System/Library/Frameworks/Python.framework/Versions/2.5/Python (compatibility version 2.5.0, current version 2.5.1) /usr//lib/libmpi_cxx.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr//lib/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.4.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) I can also use this module without problems if I import it in a script that uses /usr/bin/python2.5. Is there some environment variable that could explain the different behaviors? -- Mark Process: python2.5 [18782] Path: /Users/mmoll/Downloads/Chimera.app/Contents/Resources/bin/python2.5 Identifier: edu.ucsf.cgl.chimera Version: 1.4.0 (1.4.0.29530) Code Type: X86 (Native) Parent Process: launchd [99] Date/Time: 2009-12-08 22:37:45.424 -0600 OS Version: Mac OS X 10.6.2 (10C540) Report Version: 6 Interval Since Last Report: 134941 sec Crashes Since Last Report: 5 Per-App Interval Since Last Report: 45 sec Per-App Crashes Since Last Report: 2 Anonymous UUID: F46D9EAC-0238-44B8-87A2-7475B19DB90E Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Application Specific Information: abort() called Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 libSystem.B.dylib 0x90799732 __kill + 10 1 libSystem.B.dylib 0x90799724 kill$UNIX2003 + 32 2 libSystem.B.dylib 0x9082c98d raise + 26 3 libSystem.B.dylib 0x908429d9 __abort + 124 4 libSystem.B.dylib 0x90842a55 abort_report_np + 0 5 libstdc++.6.dylib 0x94c05fda __gnu_cxx::__verbose_terminate_handler() + 433 6 libstdc++.6.dylib 0x94c0417a __cxxabiv1::__terminate(void (*)()) + 10 7 libstdc++.6.dylib 0x94c041ba __cxxabiv1::__unexpected(void (*)()) + 0 8 libstdc++.6.dylib 0x94c042b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0 9 libstdc++.6.dylib 0x94bc0856 std::__throw_logic_error(char const*) + 158 10 libstdc++.6.dylib 0x94bebced char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) + 57 11 libstdc++.6.dylib 0x94bec1fb std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) + 53 12 _LabelHash.so 0x1a00fae4 __static_initialization_and_destruction_0(int, int) + 180 13 dyld 0x8fe0ed6d ImageLoaderMachO::doModInitFunctions(ImageLoader::LinkContext const&) + 235 14 dyld 0x8fe0d31e ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int) + 246 15 dyld 0x8fe0d3d1 ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 61 16 dyld 0x8fe0200b dyld::runInitializers(ImageLoader*) + 34 17 dyld 0x8fe0b299 dlopen + 558 18 libSystem.B.dylib 0x9073f048 dlopen + 66 19 org.python.python 0x000c6b7a _PyImport_GetDynLoadFunc + 283 (dynload_shlib.c:130) 20 org.python.python 0x000b4ed5 _PyImport_LoadDynamicModule + 107 (importdl.c:42) 21 org.python.python 0x000b2be5 load_module + 201 (import.c:1758) 22 org.python.python 0x000b30af import_submodule + 293 (import.c:2400) 23 org.python.python 0x000b32fd load_next + 195 (import.c:2220) 24 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001) 25 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072) 26 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49) 27 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861) 28 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(pythonrun.c:1273) 142 org.python.python 0x000be8a6 PyRun_SimpleFileExFlags + 640 (pythonrun.c:879) 143 org.python.python 0x000cbfce Py_Main + 3077 (main.c:523) 144 python2.5 0x000018ee _start + 216 145 python2.5 0x00001815 start + 41 Thread 1: Dispatch queue: com.apple.libdispatch-manager 0 libSystem.B.dylib 0x9075f0ea kevent + 10 1 libSystem.B.dylib 0x9075f804 _dispatch_mgr_invoke + 215 2 libSystem.B.dylib 0x9075ecc3 _dispatch_queue_invoke + 163 3 libSystem.B.dylib 0x9075ea68 _dispatch_worker_thread2 + 234 4 libSystem.B.dylib 0x9075e4f1 _pthread_wqthread + 390 5 libSystem.B.dylib 0x9075e336 start_wqthread + 30 Thread 2: 0 libSystem.B.dylib 0x9075e182 __workq_kernreturn + 10 1 libSystem.B.dylib 0x9075e718 _pthread_wqthread + 941 2 libSystem.B.dylib 0x9075e336 start_wqthread + 30 Thread 3: 0 libSystem.B.dylib 0x90774066 select$DARWIN_EXTSN$NOCANCEL + 10 1 libSystem.B.dylib 0x9080d11b select + 92 2 com.tcltk.tcllibrary 0x01900e76 TclUnixWaitForFile + 1347 3 libSystem.B.dylib 0x90765fbd 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(???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/collections.so 0x187ed000 - 0x187f4757 +libTogl2.1.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/Togl2.1/libTogl2.1.dylib 0x18ac1000 - 0x18aeefff +libTix8.4.3.dylib ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/Tix8.4.3/libTix8.4.3.dylib 0x18afe000 - 0x18c6fff7 GLEngine ??? (???) <D336658A-F6DB-6D61-9CA6-04299E7D5420> /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine 0x18ca0000 - 0x18edcfef com.apple.ATIRadeonX1000GLDriver 1.6.6 (6.0.6) <E0A5525E-5037-2D4A-0879-2FB8F865FBC2> /System/Library/Extensions/ATIRadeonX1000GLDriver.bundle/Contents/MacOS/ATIRadeonX1000GLDriver 0x18eff000 - 0x18f1bff7 GLRendererFloat ??? (???) <8FF7B576-512C-C2F8-4C0C-967FB3D9EEA2> /System/Library/Frameworks/OpenGL.framework/Resources/GLRendererFloat.bundle/GLRendererFloat 0x19015000 - 0x19023ffc +x509.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Resources/lib/x509.so 0x19031000 - 0x19032fff +icglue.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/icglue.so 0x190fe000 - 0x19101fff +_AE.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_AE.so 0x1910e000 - 0x1910ffff +_Evt.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_Evt.so 0x19117000 - 0x1911dfff +_File.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_File.so 0x193ba000 - 0x193c1ff7 mca_ns_proxy.so ??? (???) <62A3719D-F257-B6E0-86CC-64BBD8B207CA> /usr/lib/openmpi/mca_ns_proxy.so 0x193c6000 - 0x193c6ff7 mca_errmgr_hnp.so ??? (???) <3DCE56BF-2B74-B2C6-08A1-851FC9E536F2> /usr/lib/openmpi/mca_errmgr_hnp.so 0x194f8000 - 0x19503fef +datetime.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/datetime.so 0x19526000 - 0x19529fff +_Res.so ??? (???) /Users/mmoll/Downloads/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload/_Res.so 0x19738000 - 0x19746ffb libmpi_cxx.0.dylib ??? (???) <FC254088-F371-1442-3057-AD266C9FC0D6> /usr/lib/libmpi_cxx.0.dylib 0x1975c000 - 0x197a0ff7 libopen-rte.0.dylib ??? (???) <3F16BADE-3E33-E81A-1351-27AB5D5A084A> /usr/lib/libopen-rte.0.dylib 0x197b4000 - 0x197b9ff7 mca_ns_replica.so ??? (???) <B54408AC-EB76-5D46-69EB-7544AFA7AD14> /usr/lib/openmpi/mca_ns_replica.so 0x197be000 - 0x197beff7 mca_errmgr_orted.so ??? (???) <D2E4861C-5F83-E02B-87BE-790F388B0B6A> /usr/lib/openmpi/mca_errmgr_orted.so 0x197c2000 - 0x197c3ff7 mca_errmgr_proxy.so ??? (???) <2D7C420C-B47C-DE84-0853-813F8781362B> /usr/lib/openmpi/mca_errmgr_proxy.so 0x197c7000 - 0x197c7ff7 mca_rml_oob.so ??? (???) <DC93F712-FCC6-5051-EE82-4DD21D720DFA> /usr/lib/openmpi/mca_rml_oob.so 0x197cb000 - 0x197d8ff7 mca_oob_tcp.so ??? (???) <B3F70BE5-BDAD-4868-ACFE-5FF01973311D> /usr/lib/openmpi/mca_oob_tcp.so 0x197de000 - 0x197e6ff7 mca_gpr_proxy.so ??? (???) <3BC17D82-54FE-8912-BEA8-22F05549ED04> /usr/lib/openmpi/mca_gpr_proxy.so 0x197ec000 - 0x197f0ff7 mca_rds_hostfile.so ??? (???) <7D239E39-7E10-5E1F-5FBC-1D9ED0A9BAF1> /usr/lib/openmpi/mca_rds_hostfile.so 0x197f5000 - 0x197f5ff7 mca_rds_proxy.so ??? (???) <5E48AB54-1685-F0B7-2B06-27C168B211B4> /usr/lib/openmpi/mca_rds_proxy.so 0x197f9000 - 0x197fbff7 mca_rds_resfile.so ??? (???) <5F8A007F-4C83-E733-84E1-AAA2B48F0778> /usr/lib/openmpi/mca_rds_resfile.so 0x1a000000 - 0x1a64fff7 +_LabelHash.so ??? 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(???) <22885FDF-D27A-C329-5D0C-C22E8886FF80> /usr/lib/openmpi/mca_ras_xgrid.so 0x1ad13000 - 0x1ad14ff7 mca_rmaps_round_robin.so ??? (???) <75E4C219-8493-F1DB-2330-3E5AD57ECF8B> /usr/lib/openmpi/mca_rmaps_round_robin.so 0x1ad18000 - 0x1ad1aff7 mca_pls_gridengine.so ??? (???) <475CC77C-F249-0831-34C9-8B73D7729036> /usr/lib/openmpi/mca_pls_gridengine.so 0x1ad1f000 - 0x1ad21ff7 mca_pls_proxy.so ??? (???) <F2D3DDFE-07CE-9741-6ECC-22E42ABA5428> /usr/lib/openmpi/mca_pls_proxy.so 0x1ad25000 - 0x1ad29ff7 mca_pls_rsh.so ??? (???) <61F2DBD1-B245-34FC-474E-8FC73DD1A023> /usr/lib/openmpi/mca_pls_rsh.so 0x1ad2e000 - 0x1ad32ff7 mca_pls_xgrid.so ??? 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(???) <3D2C5BA3-6A8D-C861-B346-0E19942D9AF1> /usr/lib/system/libkxld.dylib 0x91768000 - 0x91832fef com.apple.CoreServices.OSServices 352 (352) <D9F21CA4-EED0-705F-8F3C-F1322D114B52> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x91833000 - 0x91934fe7 libxml2.2.dylib ??? (???) <B4C5CD68-405D-0F1B-59CA-5193D463D0EF> /usr/lib/libxml2.2.dylib 0x9194b000 - 0x9195cff7 com.apple.LangAnalysis 1.6.6 (1.6.6) <7A3862F7-3730-8F6E-A5DE-8E2CCEA979EF> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis 0x9195d000 - 0x91983fff com.apple.DictionaryServices 1.1.1 (1.1.1) <02709230-9B37-C743-6E27-3FCFD18211F8> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices 0x91984000 - 0x919beffb libFontRegistry.dylib ??? (???) <72342297-E8D6-B071-A752-014134129282> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib 0x919bf000 - 0x91a19ff7 com.apple.framework.IOKit 2.0 (???) <1BE07087-27D5-0E62-F06B-007C2BED4073> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit 0x91a1a000 - 0x91a4eff7 libssl.0.9.8.dylib ??? (???) <F3402001-EC8D-58E5-4A23-02A979C9E857> /usr/lib/libssl.0.9.8.dylib 0x91a50000 - 0x922334b7 com.apple.CoreGraphics 1.536.12 (???) <263EB5FC-DEAD-7C5B-C486-EC86C173F952> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics 0x92234000 - 0x92267ff7 com.apple.AE 496.1 (496.1) <1AC75AE2-AF94-2458-0B94-C3BB0115BA4B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE 0x92328000 - 0x92328ff7 com.apple.Cocoa 6.6 (???) <EA27B428-5904-B00B-397A-185588698BCC> /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 0x932d8000 - 0x93302ff7 com.apple.framework.Admin 4.0 (4.0) <4A434473-A6C1-3F40-2928-16CFF1222FA1> /System/Library/PrivateFrameworks/Admin.framework/Versions/A/Admin 0x93d4d000 - 0x93d9dfe7 libGLU.dylib ??? (???) <659ADCA2-10EC-59BD-1B0A-4928A965F1D1> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x93df7000 - 0x93e94fe3 com.apple.LaunchServices 362 (362) <8BE1C1A1-BF71-CE07-F3FB-6057D47AF461> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices 0x94344000 - 0x94344ff7 liblangid.dylib ??? (???) <B99607FC-5646-32C8-2C16-AFB5EA9097C2> /usr/lib/liblangid.dylib 0x94381000 - 0x9438aff7 com.apple.DiskArbitration 2.3 (2.3) <E9C40767-DA6A-6CCB-8B00-2D5706753000> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration 0x9438b000 - 0x947c0ff7 libLAPACK.dylib ??? (???) <5E2D2283-57DE-9A49-1DB0-CD027FEFA6C2> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib 0x947c1000 - 0x947c4fe7 libmathCommon.A.dylib ??? (???) <1622A54F-1A98-2CBE-B6A4-2122981A500E> /usr/lib/system/libmathCommon.A.dylib 0x947c5000 - 0x94816ff7 com.apple.HIServices 1.8.0 (???) <B8EC13DB-A81A-91BF-8C82-66E840C64C91> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices 0x94886000 - 0x94890ff7 libGL.dylib ??? (???) <76A207FE-889A-CF1B-AF9A-795EEE5A463E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x94891000 - 0x94944fff libFontParser.dylib ??? (???) <FAD5E96D-CF93-CC86-6B30-A6594B930772> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib 0x94b28000 - 0x94bb9fe7 com.apple.print.framework.PrintCore 6.1 (312.3) <6D4322AF-703C-CC19-77B4-53E6D3BB18D4> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore 0x94bba000 - 0x94c24fe7 libstdc++.6.dylib ??? (???) <411D87F4-B7E1-44EB-F201-F8B4F9227213> /usr/lib/libstdc++.6.dylib 0x94e3e000 - 0x94ee6ffb com.apple.QD 3.33 (???) <196CDBA6-5B87-2767-DD57-082D71B0A5C7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD 0x94f42000 - 0x94f42ff7 com.apple.ApplicationServices 38 (38) <8012B504-3D83-BFBB-DA65-065E061CFE03> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices 0x94fe4000 - 0x95064feb com.apple.SearchKit 1.3.0 (1.3.0) <9E18AEA5-F4B4-8BE5-EEA9-818FC4F46FD9> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit 0x9508b000 - 0x9517dff7 libcrypto.0.9.8.dylib ??? (???) <792B8722-3091-5E9F-E25F-67499CFE0599> /usr/lib/libcrypto.0.9.8.dylib 0x9517e000 - 0x9518bff7 com.apple.NetFS 3.2.1 (3.2.1) <5E61A00B-FA16-9D99-A064-47BDC5BC9A2B> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS 0x9518c000 - 0x9518dff7 com.apple.audio.units.AudioUnit 1.6.1 (1.6.1) <3A08510C-07F7-1A09-D6ED-1A488203ACCC> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit 0x9518e000 - 0x951d0fe7 libvDSP.dylib ??? (???) <8F8FFFB3-81E3-2969-5688-D5B0979182E6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib 0x951d1000 - 0x952fdfe3 com.apple.audio.toolbox.AudioToolbox 1.6.1 (1.6.1) <C226DF5C-35B0-98B8-95ED-FE5FE24E62C8> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox 0x952fe000 - 0x9530eff7 libsasl2.2.dylib ??? (???) <C8744EA3-0AB7-CD03-E639-C4F2B910BE5D> /usr/lib/libsasl2.2.dylib 0x9530f000 - 0x95405ff7 libGLProgrammability.dylib ??? (???) <82D03736-D30C-C013-BBB1-20ED9687D47F> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x95406000 - 0x954e3ff7 com.apple.vImage 4.0 (4.0) <64597E4B-F144-DBB3-F428-0EC3D9A1219E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x954e7000 - 0x954fbfe7 libbsm.0.dylib ??? (???) <14CB053A-7C47-96DA-E415-0906BA1B78C9> /usr/lib/libbsm.0.dylib 0x95535000 - 0x95576ff7 libRIP.A.dylib ??? (???) <9F0ECE75-1F03-60E4-E29C-136A27C13F2E> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib 0x95577000 - 0x95870fef com.apple.QuickTime 7.6.3 (1591.3) <803CC5FD-2369-83B5-795D-A8963620EFAC> /System/Library/Frameworks/QuickTime.framework/Versions/A/QuickTime 0x959f4000 - 0x95a16fef com.apple.DirectoryService.Framework 3.6 (621.1) <3ED4949F-9604-C109-6586-5CE5F421182B> /System/Library/Frameworks/DirectoryService.framework/Versions/A/DirectoryService 0x95a48000 - 0x95af7ff3 com.apple.ColorSync 4.6.2 (4.6.2) <F3F097AC-FDB7-3357-C64F-E28BECF4C15F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync 0x95c03000 - 0x95c0dff7 com.apple.bsd.ServiceManagement 1.0 (1.0) <B007CBE8-2539-CC71-9675-9EC04196921F> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement 0x95e49000 - 0x95e49ff7 com.apple.CoreServices 44 (44) <AC35D112-5FB9-9C8C-6189-5F5945072375> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices 0x95f16000 - 0x9632cff7 libBLAS.dylib ??? (???) <C4FB303A-DB4D-F9E8-181C-129585E59603> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 0x96354000 - 0x96366ff7 com.apple.MultitouchSupport.framework 204.9 (204.9) <B639F02B-33CC-150C-AE8C-1007EA7648F9> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport 0x96593000 - 0x967f5ff7 com.apple.security 6.0 (36910) <32B8FA26-CD73-4C45-C15A-EF8406D51FCC> /System/Library/Frameworks/Security.framework/Versions/A/Security 0x967f6000 - 0x967f9ff7 libCGXType.A.dylib ??? (???) <483FCF1C-066B-D210-7355-ABC48CA9DB2F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.dylib 0x96824000 - 0x9689efef com.apple.audio.CoreAudio 3.2.2 (3.2.2) <1F97B48A-327B-89CC-7C01-3865179716E0> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio 0x9689f000 - 0x968a6fff com.apple.print.framework.Print 6.0 (237) <7A06B15C-B835-096E-7D96-C2FE8F0D21E1> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print 0x968aa000 - 0x96a66fef com.apple.ImageIO.framework 3.0.1 (3.0.1) <598CF4F9-7542-E1A7-26D2-584933497A2E> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO 0x96a67000 - 0x96dceff7 com.apple.QuartzCore 1.6.1 (227.8) <8B90AB08-46A4-1C5C-4E71-C6AB652477B9> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore 0x96e4a000 - 0x96e6afe7 libresolv.9.dylib ??? (???) <A48921CB-3FA7-3071-AF9C-2D86FB493A3A> /usr/lib/libresolv.9.dylib 0x96fda000 - 0x97023fe7 libTIFF.dylib ??? (???) <5864AE5B-EAEB-F8B6-18FB-3D27B7895A4C> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib 0x97024000 - 0x97027ff7 libCoreVMClient.dylib ??? (???) <A89D7A78-8FB0-2BDF-30DB-A35E04A6186B> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x97028000 - 0x97075feb com.apple.DirectoryService.PasswordServerFramework 6.0 (6.0) <BF66BA5D-BBC8-78A5-DBE2-F9DE3DD1D775> /System/Library/PrivateFrameworks/PasswordServer.framework/Versions/A/PasswordServer 0x97089000 - 0x970cdfe7 com.apple.Metadata 10.6.2 (507.4) <DBCBAE7D-7B34-7806-C0B9-1E6E6D45562F> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata 0x970ce000 - 0x970eefe7 com.apple.opencl 12 (12) <2DB56F60-577B-6724-5708-7B082F62CC0F> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x970ef000 - 0x970fcff7 libbz2.1.0.dylib ??? (???) <495732E1-2AC4-44FC-E633-4CBCC503B924> /usr/lib/libbz2.1.0.dylib 0x972c6000 - 0x972c6ff7 com.apple.Carbon 150 (152) <608A04AB-F35D-D2EB-6629-16B88FB32074> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 0x97318000 - 0x9731cff7 libGIF.dylib ??? (???) <83FB0DCC-355F-A930-E570-0BD95086CC59> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib 0x9732b000 - 0x9733fffb com.apple.speech.synthesis.framework 3.10.35 (3.10.35) <57DD5458-4F24-DA7D-0927-C3321A65D743> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis 0x97340000 - 0x97343ffb com.apple.help 1.3.1 (41) <67F1F424-3983-7A2A-EC21-867BE838E90B> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help 0x97344000 - 0x97360fe3 com.apple.openscripting 1.3.1 (???) <DA16DE48-59F4-C94B-EBE3-7FAF772211A2> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting 0x97446000 - 0x97477ff3 libTrueTypeScaler.dylib ??? (???) <6C8916A2-8F85-98E0-AAD5-0020C39C0FC9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib 0x97498000 - 0x9759ffe3 com.apple.DiskImagesFramework 10.6 (281) <B57DDA36-9B4B-9D57-7072-91D531BDD2BC> /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages 0x975a0000 - 0x975aafe7 com.apple.audio.SoundManager 3.9.3 (3.9.3) <5F494955-7290-2D91-DA94-44B590191771> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/A/CarbonSound 0x9766a000 - 0x976adff7 com.apple.NavigationServices 3.5.3 (181) <28CDD978-030E-7D4A-5334-874A8EBE6C29> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/Versions/A/NavigationServices 0x976f7000 - 0x97701ffb com.apple.speech.recognition.framework 3.11.1 (3.11.1) <EC0E69C8-A121-70E8-43CF-E6FC4C7779EC> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition 0x9785c000 - 0x97863ff7 com.apple.agl 3.0.12 (AGL-3.0.12) <6BF89127-C18C-27A9-F94A-981836A822FE> /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x9789c000 - 0x9817aff7 com.apple.AppKit 6.6.3 (1038.25) <72A9AA47-8DCB-DB07-64F5-F837E98C62D8> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit 0x9817b000 - 0x9849afe7 com.apple.CoreServices.CarbonCore 861.2 (861.2) <A9077470-3786-09F2-E0C7-F082B7F97838> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore 0x9849b000 - 0x984a1fff com.apple.CommonPanels 1.2.4 (91) <2438AF5D-067B-B9FD-1248-2C9987F360BA> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels 0x9851e000 - 0x9851eff7 com.apple.Accelerate 1.5 (Accelerate 1.5) <F642E7A0-3720-FA19-0190-E6DBD9EF2D9B> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate 0x9851f000 - 0x98557ff7 com.apple.LDAPFramework 2.0 (120.1) <681A0B2E-BCB2-D2BA-3D02-A4989E9C7686> /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP 0x985a9000 - 0x986d7fe7 com.apple.CoreData 102.1 (250) <F33FF4A1-D7F9-4F6D-3153-E5F2588479EB> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData 0x986d8000 - 0x9873cffb com.apple.htmlrendering 72 (1.1.4) <4D451A35-FAB6-1288-71F6-F24A4B6E2371> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HTMLRendering.framework/Versions/A/HTMLRendering 0x9873d000 - 0x98752fff com.apple.ImageCapture 6.0 (6.0) <3F31833A-38A9-444E-02B7-17619CA6F2A0> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture 0x98753000 - 0x987a3ff7 com.apple.framework.familycontrols 2.0 (2.0) <E6CAB425-3E40-65A3-0C23-150C26E9CBBF> /System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls 0x987b8000 - 0x987edff7 libGLImage.dylib ??? (???) <A6007BF7-BF3C-96DC-C435-849C6B88C58A> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x988ca000 - 0x988ccff7 libRadiance.dylib ??? (???) <462903E2-2E77-FAE5-4ED6-829AAB1980A4> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib 0x98a4d000 - 0x98ae9fe7 com.apple.ApplicationServices.ATS 4.1 (???) <EA26375D-8276-9671-645D-D28CAEC95292> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS 0x98aea000 - 0x98b12ff7 libxslt.1.dylib ??? (???) <769EF4B2-C1AD-73D5-AAAD-1564DAEA77AF> /usr/lib/libxslt.1.dylib 0x98b35000 - 0x98b53ff7 com.apple.CoreVideo 1.6.0 (43.1) <1FB01BE0-B013-AE86-A063-481BB547D2F5> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo 0x98d0d000 - 0x98de7ff3 com.apple.DesktopServices 1.5.3 (1.5.3) <DA02AC94-7B0C-BD75-2305-C46A307A5FB0> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv 0x98de8000 - 0x98e0cff7 libJPEG.dylib ??? (???) <649E1974-A527-AC0B-B3F4-B4DC30484070> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib 0x98e0d000 - 0x98e25ff7 com.apple.CFOpenDirectory 10.6 (10.6) <1537FB4F-C112-5D12-1E5D-3B1002A4038F> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory 0x98e26000 - 0x98ea8ffb SecurityFoundation ??? (???) <29C27E0E-B2B3-BF6B-B1F8-5783B8B01535> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation 0x98eea000 - 0x98fc5ff7 com.apple.DiscRecording 5.0.3 (5030.4.2) <CC86EBA6-5E48-32C0-77AE-81479DFF6D4A> /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording 0x9900a000 - 0x99050ff7 libauto.dylib ??? (???) <85670A64-3B67-8162-D441-D8E0BE15CA94> /usr/lib/libauto.dylib 0x9908e000 - 0x990d2ff3 com.apple.coreui 2 (113) <D0FA9B36-3708-D5BF-0CC3-6CC1909BC8E6> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI 0x9920c000 - 0x992c5fe7 libsqlite3.dylib ??? (???) <16CEF8E8-8C9A-94CD-EF5D-05477844C005> /usr/lib/libsqlite3.dylib 0x992c6000 - 0x992c7ff7 com.apple.TrustEvaluationAgent 1.1 (1) <6C04C4C5-667E-2EBE-EB96-5B67BD4B2185> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x992d0000 - 0x992d4ff7 IOSurface ??? (???) <C11D3FF3-EB51-A07D-EF24-9C2004115724> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface 0x992d5000 - 0x99344ff7 libvMisc.dylib ??? (???) <59243A8C-2B98-3E71-8032-884D4853E79F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib 0x99417000 - 0x994c5ff3 com.apple.ink.framework 1.3.1 (105) <CA3FBDC3-4BBA-7BD9-0777-A7B0751292CD> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0xba900000 - 0xba916ff7 libJapaneseConverter.dylib ??? (???) <4FB5CEEB-8D3E-8C57-1718-81D7CAFBFE69> /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib 0xbab00000 - 0xbab21fe7 libKoreanConverter.dylib ??? (???) <A23F9980-5CC8-A44D-6FD6-DBFCBFF4FF28> /System/Library/CoreServices/Encodings/libKoreanConverter.dylib 0xeab00000 - 0xeab10fe7 libConverter.dylib ??? (???) <BFC392EC-73AE-D085-9D5A-63399463FD6D> /System/Library/Printers/Libraries/libConverter.dylib 0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <D45B91B2-2B4C-AAC0-8096-1FC48B7E9672> /usr/lib/libSystem.B.dylib Model: MacBookPro2,2, BootROM MBP22.00A5.B07, 2 processors, Intel Core 2 Duo, 2.33 GHz, 3 GB, SMC 1.12f5 Graphics: ATI Radeon X1600, ATY,RadeonX1600, PCIe, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x168C, 0x87), Atheros 5416: 2.0.19.4 Bluetooth: Version 2.2.4f3, 2 service, 1 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Network Service: Rice, IPSec, utun0 Serial ATA Device: Hitachi HTS541616J9SA00, 149.05 GB Parallel ATA Device: HL-DT-ST DVDRW GWA4080MA USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8501, 0xfd400000 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x021a, 0x1d200000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8205, 0x7d100000 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8240, 0x5d200000

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implementing MMTK normal calculations in chimera
by Victor Muñoz 08 Dec '09

08 Dec '09

Dear developpers, I am trying to make an extension that allows normal mode calculations with MMTK into chimera. I have several problems beginning with the following. I have first used the MMTKinter.py and added a new function called NM_ffm that calculates normal modes with a full atom force field. This works perfectly (although I am not yet able to make an animation in chimera that follows the vectors calculated...that will be a future question for you). Then I added another function (NM_mcm) that allows me to do NM calculations with the mechanical constraint (see http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/normal-mo…) For this I need to define a subspace that requires a universe.protein object (the functions are given at the end of the mail). Unfortunately, I can not pass the molecular object from the chimera space as a universe.protein object. We thought in putting self.universe.protein call into the _makeUniverse function in MMTKinter.py but that did not work. We tried other combinations but we now face the fact that we are blocked. May be we need another function in order to define subspaces but yet we still don't know how to pass chimera infos to MMTK. Could you give me a hand so that I can define correctly subspaces on chimera molecules? All the best and thank in advance for any help, Victor ************* Computational Biotechnological Chemistry @transmet ####Function for normal modes calculations in full atom ff def NM_ffm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput # from JD to make NM calculations from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys # JD'end import sys if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info(msg) replyobj.info("\n") #Calculate normal modes JD's trucho def despl(vec): run("sel #0") atoms=sele.currentAtoms() for a in atoms: a.setCoord(a.xformCoord()-10*(vec)) modes = NormalModes(self.universe) for mode in modes: print mode print mode.array L1=[] L2=[] L3=[] for mode in modes: y=6 u=len(mode.array) while y<u: L1.append(mode.array[y][0]) L2.append(mode.array[y][1]) L3.append(mode.array[y][2]) y+=1 y=0 run("sel:all") atoms=sele.currentAtoms() run("~sel") u=len(L1) a=0 o=len(atoms) while y<u: vec=Vector(float(L1[y]),float(L2[y]),float(L3[y])) atoms[a].setCoord(atoms[a].coord()-(vec)) a+=1 if a==o: a=0 raw_input() else: pass y+=1 #JD's end return modes AmberData._normalizeName = saveNormalizeName timestamp("end _minimize") ####Function for mechanical constraint def NM_mcm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from MMTK import * from MMTK.Proteins import Protein from MMTK.ForceFields import Amber94ForceField from MMTK.NormalModes import NormalModes, SubspaceNormalModes from MMTK.Subspace import RigidMotionSubspace from MMTK.Minimization import ConjugateGradientMinimizer from MMTK.Trajectory import StandardLogOutput import numpy # Victor Modifications from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys #/end if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info(msg) replyobj.info("\n") # Construct system #self.universe = InfiniteUniverse(Amber94ForceField()) #self.universe.protein = self.universe # Set up the subspace: rigid-body translation and rotation for each residue self.subspace = RigidMotionSubspace(self.universe, self.universe.protein.residues())

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MD movie for xyz format
by Jean Didier Pie Marechal 03 Dec '09

03 Dec '09

Dear all, would it be possible to have xyz format accepted for the MD movie tool. Someting identical to the PDB (with both multiple xyz file or unique xyz file containing several structures) would be more than enough. We frequently use this standard and that would be useful for us to have such possbility. All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dilluns, Novembre 23, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 70, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Rotation about the axis of symmetry (Liam Browne) > 2. Re: Rotation about the axis of symmetry (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Nov 2009 10:06:26 +0000 > From: Liam Browne <liam.browne(a)hotmail.co.uk> > To: <chimera-dev(a)cgl.ucsf.edu> > Subject: [chimera-dev] Rotation about the axis of symmetry > Message-ID: <COL124-W33C2F39CCE1734F40BEB30B69E0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > Many thanks, > Liam > > _________________________________________________________________ > View your other email accounts from your Hotmail inbox. Add them now. > http://clk.atdmt.com/UKM/go/186394592/direct/01/ >

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Rotation about the axis of symmetry
by Liam Browne 23 Nov '09

23 Nov '09

Hi all, I want to rotate a model by 90 degrees about the axis of symmetry, but I seem to be having problems setting the axis correctly. After two identical models are superimposed I use measure rotation and get the following: Matrix rotation and translation -0.04092271 -0.36724445 0.92922379 -82.20183653 -0.91203666 0.39354649 0.11537022 -54.21831923 -0.40806183 -0.84276490 -0.35104539 11.47082481 Axis -0.55288898 0.77167664 -0.31437070 Axis point -56.22800779 0.00000000 25.47389901 Rotation angle (degrees) 119.94780111 Shift along axis 0.00338820 What should I do to rotate the model at the same axis but by 90 degrees? Many thanks, Liam _________________________________________________________________ View your other email accounts from your Hotmail inbox. Add them now. http://clk.atdmt.com/UKM/go/186394592/direct/01/

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writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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writing atom information using the mol2 atom order.
by Jean Didier Pie Marechal 03 Nov '09

03 Nov '09

Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dilluns, Octubre 26, 2009 8:00 pm Assumpte: Chimera-dev Digest, Vol 69, Issue 1 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. thank you so much (Corey Fugate) > 2. Re: thank you so much (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 23 Oct 2009 16:57:11 -1000 > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] thank you so much > Message-ID: <D445EAAC-78D8-4394-85E0-997DBED43CD8(a)hawaii.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > I started using Chimera a few weeks ago. It is wonderful, I love it. > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Oct 2009 11:03:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Corey Fugate <fugate(a)hawaii.edu> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] thank you so much > Message-ID: <26F83250-86D7-4E19-8B17-304418C8169D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > So glad you like it. And always struggling to make it better. > Thanks! :-) > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 23, 2009, at 7:57 PM, Corey Fugate wrote: > > > I started using Chimera a few weeks ago. It is wonderful, I > love it. > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >

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